Related papers: Does Collective Genetic Regulation exist?
In recent years, several studies have provided insight on the functioning of the brain which consists of neurons and form networks via interconnection among them by synapses. Neural networks are formed by interconnected systems of neurons,…
We consider here the morphogenesis (pattern formation) problem for some genetic network models. First, we show that any given spatio-temporal pattern can be generated by a genetic network involving a sufficiently large number of genes.…
The question of controllability of natural and man-made network systems has recently received considerable attention. In the context of the human brain, the study of controllability may not only shed light into the organization and function…
Neural systems show a modular and typically also a hierarchical organisation across different levels and across different species. Topology relates to function, but it is also influences dynamics as earlier studies showed its effect on…
Interacting individuals in complex systems often give rise to coherent motion exhibiting coordinated global structures. Such phenomena are ubiquitously observed in nature, from cell migration, bacterial swarms, animal and insect groups, and…
Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle,…
The purpose of this paper is to abstractly describe the notion of a generative mechanism that implements a code and to provide a number of examples including the DNA-RNA machinery that implements the genetic code, Chomsky's Principles &…
We outline the global control architecture of genomes. A theory of genomic control information is presented. The concept of a developmental control network called a cene (for control gene) is introduced. We distinguish parts-genes from…
Gene regulatory networks arise in all living cells, allowing the control of gene expression patterns. The study of their topology has revealed that certain subgraphs of interactions or "motifs" appear at anomalously high frequencies. We ask…
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated…
Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell…
Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this work we investigate these properties within an artificial genome model originally…
Collective decision-making enables multi-robot systems to act autonomously in real-world environments. Existing collective decision-making mechanisms suffer from the so-called speed versus accuracy trade-off or rely on high complexity,…
The success of Deep Learning methods is not well understood, though various attempts at explaining it have been made, typically centered on properties of stochastic gradient descent. Even less clear is why certain neural network…
In societal-scale decision-making systems the collective is faced with the problem of ensuring that the derived group decision is in accord with the collective's intention. In modern systems, political institutions have instatiated…
Machine learning can have major societal impact in computational biology applications. In particular, it plays a central role in the development of precision medicine, whereby treatment is tailored to the clinical or genetic features of the…
Genetic regulatory networks are usually modeled by systems of coupled differential equations and by finite state models, better known as logical networks, are also used. In this paper we consider a class of models of regulatory networks…
The biological processes of cellular decision making and differentiation involve a plethora of signalling pathways and gene regulatory circuits. These networks, in their turn, exhibit a multitude of motifs playing crucial parts in…